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CUTseq is a versatile method for preparing multiplexed DNA sequencing libraries from low-input samples

Author

Listed:
  • Xiaolu Zhang

    (Karolinska Institutet)

  • Silvano Garnerone

    (Karolinska Institutet)

  • Michele Simonetti

    (Karolinska Institutet)

  • Luuk Harbers

    (Karolinska Institutet)

  • Marcin Nicoś

    (Karolinska Institutet
    Medical University of Lublin)

  • Reza Mirzazadeh

    (Karolinska Institutet)

  • Tiziana Venesio

    (Candiolo Cancer Institute, FPO-IRCCS)

  • Anna Sapino

    (Candiolo Cancer Institute, FPO-IRCCS
    University of Turin)

  • Johan Hartman

    (Karolinska Institutet
    Karolinska University Laboratory)

  • Caterina Marchiò

    (Candiolo Cancer Institute, FPO-IRCCS
    University of Turin)

  • Magda Bienko

    (Karolinska Institutet)

  • Nicola Crosetto

    (Karolinska Institutet)

Abstract

Current multiplexing strategies for massively parallel sequencing of genomic DNA mainly rely on library indexing in the final steps of library preparation. This procedure is costly and time-consuming, because a library must be generated separately for each sample. Furthermore, library preparation is challenging in the case of fixed samples, such as DNA extracted from formalin-fixed paraffin-embedded (FFPE) tissues. Here we describe CUTseq, a method that uses restriction enzymes and in vitro transcription to barcode and amplify genomic DNA prior to library construction. We thoroughly assess the sensitivity and reproducibility of CUTseq in both cell lines and FFPE samples, and demonstrate an application of CUTseq for multi-region DNA copy number profiling within single FFPE tumor sections, to assess intratumor genetic heterogeneity at high spatial resolution. In conclusion, CUTseq is a versatile and cost-effective method for library preparation for reduced representation genome sequencing, which can find numerous applications in research and diagnostics.

Suggested Citation

  • Xiaolu Zhang & Silvano Garnerone & Michele Simonetti & Luuk Harbers & Marcin Nicoś & Reza Mirzazadeh & Tiziana Venesio & Anna Sapino & Johan Hartman & Caterina Marchiò & Magda Bienko & Nicola Crosetto, 2019. "CUTseq is a versatile method for preparing multiplexed DNA sequencing libraries from low-input samples," Nature Communications, Nature, vol. 10(1), pages 1-12, December.
    • Handle: RePEc:nat:natcom:v:10:y:2019:i:1:d:10.1038_s41467-019-12570-2
    DOI: 10.1038/s41467-019-12570-2
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    Cited by:

    1. Ning Zhang & Luuk Harbers & Michele Simonetti & Constantin Diekmann & Quentin Verron & Enrico Berrino & Sara E. Bellomo & Gabriel M. C. Longo & Michael Ratz & Niklas Schultz & Firas Tarish & Peng Su &, 2024. "High clonal diversity and spatial genetic admixture in early prostate cancer and surrounding normal tissue," Nature Communications, Nature, vol. 15(1), pages 1-17, December.

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